#include <iostream>
#include <sstream>
#include "Chromosome.hpp"
#include "SyntenyFinder.hpp"

int main(int argc, char* argv[]) {
	std::string inputFileName;
	if (argc == 2) {
		inputFileName = argv[1];
	}
	else {
		std::cerr << "usage: " << argv[0] << " [inputFileName]" << std::endl;
		return 1;
	}
	synteny::SyntenyFinder syntenyFinder;
	if(syntenyFinder.loadChromosomes(inputFileName)) {
		std::cout << "Can't load chromosomes!" << std::endl;
		return 1;
	}
	syntenyFinder.modifySequence(12, 10);

	return 0;
}
